Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes
Published 2016 View Full Article
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Title
Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes
Authors
Keywords
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Journal
Frontiers in Microbiology
Volume 7, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2016-04-12
DOI
10.3389/fmicb.2016.00469
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Note: Only part of the references are listed.- MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
- (2015) Dinghua Li et al. BIOINFORMATICS
- Sewage Reflects the Microbiomes of Human Populations
- (2015) Ryan J. Newton et al. mBio
- MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
- (2015) Dongwan D. Kang et al. PeerJ
- Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
- (2014) Jorge F Vázquez-Castellanos et al. BMC GENOMICS
- Classification and quantification of bacteriophage taxa in human gut metagenomes
- (2014) Alison S Waller et al. ISME Journal
- Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
- (2014) H Bjørn Nielsen et al. NATURE BIOTECHNOLOGY
- Binning metagenomic contigs by coverage and composition
- (2014) Johannes Alneberg et al. NATURE METHODS
- Understanding How Commensal Obligate Anaerobic Bacteria Regulate Immune Functions in the Large Intestine
- (2014) Eva Maier et al. Nutrients
- Assembly of viral genomes from metagenomes
- (2014) Saskia L. Smits et al. Frontiers in Microbiology
- Kraken: ultrafast metagenomic sequence classification using exact alignments
- (2014) Derrick E Wood et al. GENOME BIOLOGY
- GroopM: an automated tool for the recovery of population genomes from related metagenomes
- (2014) Michael Imelfort et al. PeerJ
- MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
- (2014) Yu-Wei Wu et al. Microbiome
- Oxidative Stress at High Temperatures in Lactococcus lactis Due to an Insufficient Supply of Riboflavin
- (2013) Jun Chen et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
- (2013) Mads Albertsen et al. NATURE BIOTECHNOLOGY
- Genomes from Metagenomics
- (2013) I. Sharon et al. SCIENCE
- Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment
- (2013) Cindy J. Castelle et al. Nature Communications
- The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
- (2013) Sara C Di Rienzi et al. eLife
- IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
- (2012) Y. Peng et al. BIOINFORMATICS
- Taxonomic binning of metagenome samples generated by next-generation sequencing technologies
- (2012) J. Droge et al. BRIEFINGS IN BIOINFORMATICS
- Comparison of Next-Generation Sequencing Systems
- (2012) Lin Liu et al. JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY
- Metagenomic microbial community profiling using unique clade-specific marker genes
- (2012) Nicola Segata et al. NATURE METHODS
- MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
- (2012) Toshiaki Namiki et al. NUCLEIC ACIDS RESEARCH
- Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
- (2012) Daniel R. Mende et al. PLoS One
- Fast and Accurate Taxonomic Assignments of Metagenomic Sequences Using MetaBin
- (2012) Vineet K. Sharma et al. PLoS One
- Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
- (2012) K. C. Wrighton et al. SCIENCE
- Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota
- (2012) V. Iverson et al. SCIENCE
- Metagenomics and future perspectives in virus discovery
- (2012) John L Mokili et al. Current Opinion in Virology
- SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
- (2012) Ruibang Luo et al. GigaScience
- Meta-IDBA: a de Novo assembler for metagenomic data
- (2011) Y. Peng et al. BIOINFORMATICS
- Bambus 2: scaffolding metagenomes
- (2011) Sergey Koren et al. BIOINFORMATICS
- ART: a next-generation sequencing read simulator
- (2011) Weichun Huang et al. BIOINFORMATICS
- FLASH: fast length adjustment of short reads to improve genome assemblies
- (2011) T. Magoc et al. BIOINFORMATICS
- BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
- (2011) Nabil-Fareed Alikhan et al. BMC GENOMICS
- The human gut virome: Inter-individual variation and dynamic response to diet
- (2011) S. Minot et al. GENOME RESEARCH
- Individual genome assembly from complex community short-read metagenomic datasets
- (2011) Chengwei Luo et al. ISME Journal
- Genovo: De Novo Assembly for Metagenomes
- (2011) Jonathan Laserson et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Efficient de novo assembly of single-cell bacterial genomes from short-read data sets
- (2011) Hamidreza Chitsaz et al. NATURE BIOTECHNOLOGY
- Taxonomic metagenome sequence assignment with structured output models
- (2011) Kaustubh R Patil et al. NATURE METHODS
- Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
- (2011) M. Hess et al. SCIENCE
- Bacterial biogeography of the human digestive tract
- (2011) Jennifer C. Stearns et al. Scientific Reports
- A human gut microbial gene catalogue established by metagenomic sequencing
- (2010) Junjie Qin et al. NATURE
- Ab initio gene identification in metagenomic sequences
- (2010) Wenhan Zhu et al. NUCLEIC ACIDS RESEARCH
- SOAP2: an improved ultrafast tool for short read alignment
- (2009) R. Li et al. BIOINFORMATICS
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
- (2009) Naryttza N Diaz et al. BMC BIOINFORMATICS
- Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
- (2009) Arthur Brady et al. NATURE METHODS
- Genome Project Standards in a New Era of Sequencing
- (2009) P. S. G. Chain et al. SCIENCE
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
- Mapping short DNA sequencing reads and calling variants using mapping quality scores
- (2008) H. Li et al. GENOME RESEARCH
- Bacteria in the Intestine, Helpful Residents or Enemies from Within?
- (2008) G. O. Canny et al. INFECTION AND IMMUNITY
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